SDK for GPU accelerated genome assembly and analysis
Updated tqdm requirements for pygenomeworks.
Updated numpy and cython requirements for pygenomeworks.
CUDA Mapper
CUDA Aligner
=
and mismatches X
.create_aligner()
are the banded Myers aligner (a FixedBandAligner) for the create_aligner()
function that does specify a bandwidth and Hirschberg-Myers aligner (a Aligner) for the create_aligner()
call that does not specify a bandwidth. The API for the latter case is deprecated in will be replaced by a different create_aligner()
function.CUDA Partial Order Aligner (CUDA POA)
-s
for CUDA POA API to allow managing allocated memory for adaptive score matrixstatic_band_traceback
as a new alignment mode in CUDA POA. This mode can potentially improve performance for processing long-read batches.adaptive_band_traceback
for long-read batches. Different banded versions of Needleman-Wunsch kernels were unified.CUDA Extender
Pygenomeworks
Other
DevicePreallocatedAllocator
allocates exactly the amount of memory requestedHOTFIX - Fixes to unblock GCC 9 and CUDA 11 beta support.
HOTFIX - Fixed an integer overflow in cudaaligner.
HOTFIX - Updated CMake structure to enable better integration with external tools.
Release v0.5.0 brings major performance and functionality updates to all modules with a focus on improved handling of long read sequences.
GenomeWorks
. The python bindings package is now available on PyPI as genomeworks
.cudaaligner
performance of long read global alignment (10-15kb sequences) by ~3x over previous implementations with comparable accuracy. Narrow bands may lead to non-optimal alignments.Alignment
object provides edit distance for each alignment and a new flag to signal optimal vs non-optimal alignments.cudamapper
APIs to build a GPU-accelerated, minimizer based mapper.cmake
default installation path mechanismRelease candidate for v0.5.0 focuses primarily on improving the performance of the GPU accelerated mapper, cudamapper . Here are some highlights of this release so far -
-F
option. More details highlighted in help message)-C
and -c
)Application | dataset | GPU | v0.4.3 | v0.5.0-rc1 | Acceleration |
---|---|---|---|---|---|
cudamapper all-vs-all | ONT E. Coli 150x | 1x GV100 32GB | 72.3s | 23.2s | 3.11x |
Release 0.4.3 is a hotfix for wheel package generation in Puyclaragenomics.
liblogging.so
linkage error occurred in Python 3.5.